First of all Railways are the most economical mode of transportation in the country especially the freight traffic. Doubling of tracks will definately be helpful economically which is the need of the hour now in Goa. After the ban on mining in Goa the economy has suffered badly and due to which many people depended on mining and related sectors lost their jobs and businesses.
And this is not the only project that is opposed people are also opposing the widening of NH4A highway, IIT project, Mopa Airport, restating of mining, etc. and on the other hand the same people are hammering the government night and day for not providing jobs and the falling economy.
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doubling is cleared by both Goa and Karnataka forest departments and I don't think adding a second line on the already existing route would damage natural beauty.
Moreover now due to lack of jobs or good salaries many Goans are moving to other countries I can name atleast 100 people who I know working in Golf, UK or on cruises I myself am personally trying past two years for a job at UAE as it's difficult to sustain a decent life in Goa.
These people opposing also are supported by a group called Revolutionary Goans which is utterly racist they call all non Goans as "Ghatis" means one coming from the Ghats and sorry for saying it's you also as per them, that group's main motto is to form a regional party through which they can enter politics and they are all around doing selective outrages in which some migrants are doing some misdeeds or criminal activities and portraying an image to Goans that migrants are bad and need to be kicked out of the state of Goa and whole Goa belongs to Goans only so it's natural that when people are brainwashed by such ideas they will oppose any kind of development project as it will definitely bring in more migrants due to the growing economic activities.
In the end I would say it's more political especially regional politics and attitude of some Goans towards non Goans that people are opposing any kind of development projects without realising that it would be Goa which would suffer ultimately.
All this is coming from myself who is a native Goan.